Web Services

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Findex.html;h=d0b497c611ecf9f5655a0a52aec40481f07ce404;hb=31117f8593d9c51c6238be3d40771819da96939d;hp=939db64b05cdcd832ddb1b813f307d508cf252ac;hpb=0696cffbccbb537be78d9fc2410589adbcd7be35;p=jalview.git diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html index 939db64..d0b497c 100755 --- a/help/html/webServices/index.html +++ b/help/html/webServices/index.html @@ -1,114 +1,93 @@ - + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> Web Services -

Web services

- -

Jalview includes clients for a variety of web services for both -bioinformatic data retrieval and analysis. -

The Sequence Fetcher - utilises web services for sequence, alignment and structure retrieval - provided by the European Bioinformatics Institute (EBI) and Distributed - Annotation System servers that are capable of serving sequences.
The DAS Feature - Fetcher enables the retrieval and visualization of features from DAS - annotation sources
The Database Reference Fetcher - transfers database references from records available from DAS or the - public sequence databases.
The Web Services menu in each alignment - window also provides access to the following: -
- Jalview SOAP Web Services for sequence alignment and - secondary structure prediction based at the University of Dundee.
- Services for submitting IDs and sequences to external - bioinformatics services such as Envision2.
- Programs for multiple sequence alignment, made available via - Java Bioinformatic Analysis Web Service - (JABAWS) servers.
- The Web Services Preference panel - controls the display and appearance of the submission and analysis - services in the Web Services menu.
If Jalview encounters problems accessing any services, it may - display a warning dialog - box (this can be turned off using the web services preferences tab).

More about Jalview's Web Services
-Jalview's distributed computations are SOAP based services exposing -protein sequence alignment and secondary structure prediction programs. -These services actually run on the cluster based in the School of Life -Sciences, University of Dundee, and are maintained by the Barton group.

Envision2 Services

Since version 2.5, Jalview has included a client to enable the -user to submit one or more sequences or sequence IDs to analysis -workflows provided by the EnVision2 web -application. This allows Jalview users to easily access the EnCore -network of databases and analysis services developed by ENFIN (www.enfin.org).

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Web Service Dialog Box

This dialog box is displayed when a web service job is submitted. -It gives the name of the service and any method citation information, -and monitors the progress of the calculation. The cancel button will -permanently cancel the job, but this is only possible for some services. -

Current services: -

Multiple Sequence - Alignment Services

ClustalW Multiple Alignment and - re-alignment
- The clustal W service remains one of the more popular Jalview - features.
Muscle Multiple Alignment
- High Quality and High Throughput multiple alignments of proteins. This - method can sometimes be more accurate than ClustalW when dealing with - diverse sets of sequences.
MAFFT
- Multiple Alignment with Fast Fourier Transforms - a highly accurate - and high throughput dna and amino acid alignment method, performing at - least as well as ClustalW and Muscle.
Other alignment methods are also available via JABAWS. For more information about a - particular service, see the documentation available via the web services parameter dialog box.

Secondary Structure Prediction -
- JNet
  - This is a front end to the JNet www server - allowing single sequence or profile based prediction.
-

+ Web services +

Jalview includes clients for a variety of web services for both + bioinformatic data retrieval and analysis. +

The Sequence + Fetcher utilises web services for sequence, alignment and + structure retrieval provided by the European Bioinformatics + Institute (EBI) and Distributed Annotation System servers that are + capable of serving sequences. +
The DAS Feature + Fetcher enables the retrieval and visualization of features from + DAS annotation sources +
The Database Reference + Fetcher transfers database references from records available + from DAS or the public sequence databases. +
The Web Services menu in each alignment + window also provides access to the following: +
- Programs for multiple + sequence alignment, made available via Java Bioinformatic Analysis + Web Service (JABAWS) servers. +
- Jalview SOAP Web Services for secondary + structure prediction based at the University of Dundee. +
- Services for alignment analysis, such as Multi-Harmony. +
+
+ Web Service Dialog Box +
+
This dialog box is displayed when a web service job is + submitted. It gives the name of the service and any method + citation information, and monitors the progress of the + calculation. The cancel button will permanently cancel the job, + but this is only possible for some services.
The Web Services Preference + panel controls the display and appearance of the submission and + analysis services in the Web Services menu. +
If Jalview encounters problems accessing any services, it + may display a warning + dialog box (this can be turned off using the web services + preferences tab). +

+ More about Jalview's Web Services
+ Jalview's distributed computations utilise SOAP and REST + web services exposing sequence alignment, analysis, and secondary + structure prediction programs. Originally, Jalview 2's services were + maintained by the Barton group at the University of Dundee, and ran + programs on the Life Sciences High-performance Computing Cluster. + With the advent of JABAWS, + however, it is possible for anyone to host Jalview web services. +